Merge remote-tracking branch 'remotes/origin/develop' into feature-snp_test

external-example/pom.xml

pom.xml

protected/biopet-gatk-extensions/pom.xml

protected/biopet-gatk-pipelines/pom.xml

...iopet/pipelines/gatk/variantcallers/HaplotypeCaller.scala

...pipelines/gatk/variantcallers/HaplotypeCallerAllele.scala

...t/pipelines/gatk/variantcallers/HaplotypeCallerGvcf.scala

...opet/pipelines/gatk/variantcallers/UnifiedGenotyper.scala

...ipelines/gatk/variantcallers/UnifiedGenotyperAllele.scala

protected/biopet-protected-package/pom.xml

protected/pom.xml

public/bam2wig/pom.xml

...a/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala

public/bammetrics/pom.xml

...lumc/sasc/biopet/pipelines/bammetrics/TargetRegions.scala

public/basty/pom.xml

public/biopet-core/pom.xml

...s/nl/lumc/sasc/biopet/core/report/ext/js/d3.v3.5.5.min.js

...e/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala

...la/nl/lumc/sasc/biopet/core/annotations/Annotations.scala